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Question: Bioconductor / COHCAP GitHub Update
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gravatar for cwarden45
3 months ago by
cwarden450
United States
cwarden450 wrote:

Hi,

I downloaded code for the COHCAP Bioconductor SVN repository (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP/), made some changes, and then tried to commit those changes.  However, I got an error message that the SVN repository is locked, so the changes could not be uploaded because of a switch to git.

I have a GitHub account, and I uploaded the COHCAP code (with the latest round of changes) to GitHub:

https://github.com/cwarden45/COHCAP

However, I am not sure how to make this the new Bioconductor repository.  I am trying to follow the instructions available here:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

However, if I run the command git remote add upstream git@git.bioconductor.org:packages/COHCAP.git, then I get an error message: fatal: Not a git repository.

Can you please help me update the COHCAP Bioconductor repository and understand how this is now managed through GitHub?

Thanks,

Charles

ADD COMMENTlink written 3 months ago by cwarden450
1

Did you run the git remote add command in the package root dir? I see a similar error message when I try to run a git command but I've forgotten to cd into the package directory.

ADD REPLYlink modified 3 months ago • written 3 months ago by Andrzej Oleś670

Thanks for the suggestion - I did need to cd into the COHCAP directory.

I also needed to create a ssh key and submit it to Bioconductor using this form.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by cwarden450
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